Starting phenix.real_space_refine
on Wed Aug  5 04:52:41 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9yg5_72913/08_2026/9yg5_72913.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yg5_72913/08_2026/9yg5_72913.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yg5_72913/08_2026/9yg5_72913.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yg5_72913/08_2026/9yg5_72913.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yg5_72913/08_2026/9yg5_72913.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yg5_72913/08_2026/9yg5_72913.cif"
  }
  resolution = 3.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    5393      2.51       5
     N    1356      2.21       5
     O    1453      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8250
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 3103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3103
          Classifications: {'peptide': 384}
          Link IDs: {'PTRANS': 14, 'TRANS': 369}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 636, 5147
          Classifications: {'peptide': 636}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 604}
          Chain breaks: 6
  Time building chain proxies: 1.84, per 1000 atoms: 0.22
  Number of scatterers: 8250
  At special positions: 0
  Unit cell: (125.632, 150.592, 99.008, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1453      8.00
     N    1356      7.00
     C    5393      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 369.3 milliseconds
  

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 8 sheets defined
      38.7% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'D' and resid 4 through 32
      removed outlier: 3.722A  pdb=" N   LEU D   8 " --> pdb=" O   PRO D   4 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 59
      Proline residue:  D  47  - end of helix
      removed outlier: 3.678A  pdb=" N   HIS D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 75
    Processing helix  chain 'D' and resid 77 through 93
    Processing helix  chain 'D' and resid 124 through 146
      removed outlier: 3.533A  pdb=" N   LEU D 146 " --> pdb=" O   ILE D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 148 through 161
    Processing helix  chain 'D' and resid 166 through 196
      removed outlier: 3.674A  pdb=" N   LEU D 178 " --> pdb=" O   THR D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 233
      removed outlier: 3.832A  pdb=" N   VAL D 232 " --> pdb=" O   LEU D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 237 through 260
      removed outlier: 3.923A  pdb=" N   ILE D 241 " --> pdb=" O   VAL D 237 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE D 243 " --> pdb=" O   VAL D 239 " (cutoff:3.500A)
      Proline residue:  D 252  - end of helix
    Processing helix  chain 'D' and resid 272 through 294
    Processing helix  chain 'D' and resid 313 through 338
      removed outlier: 3.669A  pdb=" N   LEU D 317 " --> pdb=" O   ASN D 313 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   VAL D 319 " --> pdb=" O   TYR D 315 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 340 through 346
      removed outlier: 3.580A  pdb=" N   TYR D 343 " --> pdb=" O   THR D 340 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   TYR D 345 " --> pdb=" O   ILE D 342 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 347 through 373
    Processing helix  chain 'B' and resid 1611 through 1615
    Processing helix  chain 'B' and resid 1654 through 1669
    Processing helix  chain 'B' and resid 1736 through 1740
      removed outlier: 3.593A  pdb=" N   ARG B1740 " --> pdb=" O   ILE B1737 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1847 through 1866
    Processing helix  chain 'B' and resid 2570 through 2586
    Processing helix  chain 'B' and resid 2674 through 2678
    Processing helix  chain 'B' and resid 2717 through 2728
    Processing helix  chain 'B' and resid 3052 through 3064
    Processing helix  chain 'B' and resid 3153 through 3167
      removed outlier: 3.550A  pdb=" N   THR B3162 " --> pdb=" O   ARG B3158 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 122 through 123
    Processing sheet with id=AA2, first strand: chain 'D' and resid 105 through 107
    Processing sheet with id=AA3, first strand: chain 'D' and resid 299 through 300
      removed outlier: 4.827A  pdb=" N   GLN D 299 " --> pdb=" O   SER D 309 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 1552 through 1559
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 1552 through 1559
    current: chain 'B' and resid 1576 through 1589
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 1594 through 1598
    current: chain 'B' and resid 1621 through 1626
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1640 through 1653
      removed outlier: 6.955A  pdb=" N   VAL B1641 " --> pdb=" O   GLU B1720 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ILE B1722 " --> pdb=" O   VAL B1641 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ASP B1643 " --> pdb=" O   ILE B1722 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   MET B1724 " --> pdb=" O   ASP B1643 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   SER B1645 " --> pdb=" O   MET B1724 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ILE B1726 " --> pdb=" O   SER B1645 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   LYS B1647 " --> pdb=" O   ILE B1726 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE B1730 " --> pdb=" O   LEU B1649 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   SER B1728 " --> pdb=" O   SER B1749 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   SER B1749 " --> pdb=" O   SER B1728 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   PHE B1730 " --> pdb=" O   ALA B1747 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   ALA B1747 " --> pdb=" O   PHE B1730 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   VAL B1732 " --> pdb=" O   LEU B1745 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU B1745 " --> pdb=" O   VAL B1732 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   GLU B1734 " --> pdb=" O   PRO B1743 " (cutoff:3.500A)
      removed outlier: 5.665A  pdb=" N   MET B1744 " --> pdb=" O   TYR B1775 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   TYR B1774 " --> pdb=" O   PRO B1784 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ASN B1776 " --> pdb=" O   TRP B1782 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   TRP B1782 " --> pdb=" O   ASN B1776 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 1781 through 1786
    current: chain 'B' and resid 1830 through 1846
      removed outlier: 6.057A  pdb=" N   THR B1831 " --> pdb=" O   GLN B2522 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   ILE B2524 " --> pdb=" O   THR B1831 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   ILE B1833 " --> pdb=" O   ILE B2524 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   VAL B2526 " --> pdb=" O   ILE B1833 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   PHE B1835 " --> pdb=" O   VAL B2526 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   LEU B2528 " --> pdb=" O   PHE B1835 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   SER B1837 " --> pdb=" O   LEU B2528 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ASP B2530 " --> pdb=" O   SER B1837 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ASP B1839 " --> pdb=" O   ASP B2530 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   GLY B2532 " --> pdb=" O   ASP B1839 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LEU B1841 " --> pdb=" O   GLY B2532 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   SER B2534 " --> pdb=" O   LEU B1841 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ILE B1843 " --> pdb=" O   SER B2534 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   VAL B2536 " --> pdb=" O   ILE B1843 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LEU B1845 " --> pdb=" O   VAL B2536 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ASN B2537 " --> pdb=" O   GLU B2543 " (cutoff:3.500A)
      removed outlier: 5.363A  pdb=" N   GLU B2543 " --> pdb=" O   ASN B2537 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 2542 through 2550
    current: chain 'B' and resid 2640 through 2647
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 2640 through 2647
    current: chain 'B' and resid 2663 through 2667
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 2663 through 2667
    current: chain 'B' and resid 2699 through 2708
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 2699 through 2708
    current: chain 'B' and resid 2822 through 2824
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1789 through 1790
    Processing sheet with id=AA7, first strand: chain 'B' and resid 2567 through 2568
      removed outlier: 3.978A  pdb=" N   ALA B2621 " --> pdb=" O   LYS B2559 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LYS B2613 " --> pdb=" O   ARG B2604 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL B2601 " --> pdb=" O   LEU B2597 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 3075 through 3079
      removed outlier: 6.860A  pdb=" N   ILE B3089 " --> pdb=" O   PHE B3076 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   HIS B3078 " --> pdb=" O   LEU B3087 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LEU B3087 " --> pdb=" O   HIS B3078 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   GLY B3093 " --> pdb=" O   THR B3090 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL B3094 " --> pdb=" O   GLN B3110 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   GLN B3110 " --> pdb=" O   VAL B3094 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   PHE B3096 " --> pdb=" O   GLU B3108 " (cutoff:3.500A)

    368 hydrogen bonds defined for protein.
    1053 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.15

  Time building geometry restraints manager: 0.85 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 2539
        1.34 -     1.46: 1482
        1.46 -     1.57: 4340
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 8439
  Sorted by residual:
  bond pdb=" CG1 ILE D 142 "
       pdb=" CD1 ILE D 142 "
    ideal  model  delta    sigma   weight residual
    1.513  1.469  0.044 3.90e-02 6.57e+02 1.25e+00
  bond pdb=" CG  GLN D 354 "
       pdb=" CD  GLN D 354 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.18e+00
  bond pdb=" CB  GLU B3166 "
       pdb=" CG  GLU B3166 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.86e-01
  bond pdb=" CA  ASN D  96 "
       pdb=" CB  ASN D  96 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.67e-01
  bond pdb=" CB  ASN D  96 "
       pdb=" CG  ASN D  96 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.41e-01
  ... (remaining 8434 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.69: 11320
        2.69 -     5.37: 91
        5.37 -     8.06: 12
        8.06 -    10.75: 4
       10.75 -    13.44: 1
  Bond angle restraints: 11428
  Sorted by residual:
  angle pdb=" CA  LEU D 285 "
        pdb=" CB  LEU D 285 "
        pdb=" CG  LEU D 285 "
      ideal   model   delta    sigma   weight residual
     116.30  129.74  -13.44 3.50e+00 8.16e-02 1.47e+01
  angle pdb=" CA  GLU B3166 "
        pdb=" CB  GLU B3166 "
        pdb=" CG  GLU B3166 "
      ideal   model   delta    sigma   weight residual
     114.10  120.53   -6.43 2.00e+00 2.50e-01 1.03e+01
  angle pdb=" N   GLN D 354 "
        pdb=" CA  GLN D 354 "
        pdb=" CB  GLN D 354 "
      ideal   model   delta    sigma   weight residual
     110.28  115.10   -4.82 1.55e+00 4.16e-01 9.69e+00
  angle pdb=" N   THR D 288 "
        pdb=" CA  THR D 288 "
        pdb=" CB  THR D 288 "
      ideal   model   delta    sigma   weight residual
     110.16  114.61   -4.45 1.48e+00 4.57e-01 9.04e+00
  angle pdb=" CA  LEU D  75 "
        pdb=" CB  LEU D  75 "
        pdb=" CG  LEU D  75 "
      ideal   model   delta    sigma   weight residual
     116.30  126.68  -10.38 3.50e+00 8.16e-02 8.79e+00
  ... (remaining 11423 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 4410
       17.52 -    35.03: 510
       35.03 -    52.54: 115
       52.54 -    70.06: 26
       70.06 -    87.57: 9
  Dihedral angle restraints: 5070
    sinusoidal: 2064
      harmonic: 3006
  Sorted by residual:
  dihedral pdb=" CA  SER D 148 "
           pdb=" C   SER D 148 "
           pdb=" N   ALA D 149 "
           pdb=" CA  ALA D 149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.82   17.18     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  ILE B3122 "
           pdb=" C   ILE B3122 "
           pdb=" N   VAL B3123 "
           pdb=" CA  VAL B3123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.10  -16.90     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  PHE D 248 "
           pdb=" C   PHE D 248 "
           pdb=" N   PHE D 249 "
           pdb=" CA  PHE D 249 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.62   16.38     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 5067 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 796
       0.031 -    0.062: 328
       0.062 -    0.093: 112
       0.093 -    0.124: 76
       0.124 -    0.155: 10
  Chirality restraints: 1322
  Sorted by residual:
  chirality pdb=" CB  THR D  54 "
            pdb=" CA  THR D  54 "
            pdb=" OG1 THR D  54 "
            pdb=" CG2 THR D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 6.00e-01
  chirality pdb=" CB  ILE B3122 "
            pdb=" CA  ILE B3122 "
            pdb=" CG1 ILE B3122 "
            pdb=" CG2 ILE B3122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.40e-01
  chirality pdb=" CA  GLN D 354 "
            pdb=" N   GLN D 354 "
            pdb=" C   GLN D 354 "
            pdb=" CB  GLN D 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.33e-01
  ... (remaining 1319 not shown)

  Planarity restraints: 1407
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 245 "   -0.020 2.00e-02 2.50e+03   2.10e-02 7.74e+00
        pdb=" CG  PHE D 245 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 245 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 245 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 245 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 245 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 245 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B3166 "   -0.007 2.00e-02 2.50e+03   1.52e-02 2.30e+00
        pdb=" CD  GLU B3166 "    0.026 2.00e-02 2.50e+03
        pdb=" OE1 GLU B3166 "   -0.009 2.00e-02 2.50e+03
        pdb=" OE2 GLU B3166 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D 109 "    0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO D 110 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO D 110 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D 110 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1404 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.62: 12
        2.62 -     3.19: 7257
        3.19 -     3.76: 13074
        3.76 -     4.33: 17173
        4.33 -     4.90: 28411
  Nonbonded interactions: 65927
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D 327 "
            pdb=" CD1 LEU D 331 "
     model   vdw
     2.044 3.460
  nonbonded pdb=" CG1 VAL D 225 "
            pdb=" OD1 ASN D 328 "
     model   vdw
     2.092 3.460
  nonbonded pdb=" CD1 LEU B3087 "
            pdb=" O   LEU B3095 "
     model   vdw
     2.184 3.460
  nonbonded pdb=" CG1 VAL B3097 "
            pdb=" CD1 LEU B3105 "
     model   vdw
     2.265 3.880
  nonbonded pdb=" SG  CYS D 347 "
            pdb=" CB  LEU D 350 "
     model   vdw
     2.343 3.800
  ... (remaining 65922 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             25.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.690
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8439  Z= 0.142
  Angle     :  0.640  13.437  11428  Z= 0.317
  Chirality :  0.044   0.155   1322
  Planarity :  0.004   0.054   1407
  Dihedral  : 16.031  87.574   3114
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 21.49 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.28), residues: 1002
  helix:  1.96 (0.26), residues: 372
  sheet: -0.67 (0.31), residues: 302
  loop : -1.07 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 215 
 TYR   0.016   0.001   TYR B3073 
 PHE   0.049   0.001   PHE D 245 
 TRP   0.006   0.001   TRP D 295 
 HIS   0.004   0.001   HIS D 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.14 ( 8439)
  covalent geometry    : angle       0.63970 /  0.32 (11428)
  hydrogen bonds       : bond        0.11812 /  8.54 (  368)
  hydrogen bonds       : angle       5.83321 /  4.00 ( 1053)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.226 
Fit side-chains
REVERT: D   17 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7085 (tm-30)
REVERT: D  120 LYS cc_start: 0.8252 (mmtt) cc_final: 0.7996 (mmtt)
REVERT: D  164 ASP cc_start: 0.6166 (m-30) cc_final: 0.5952 (t0)
REVERT: D  199 TYR cc_start: 0.8131 (m-80) cc_final: 0.7676 (m-80)
REVERT: D  284 THR cc_start: 0.8462 (m) cc_final: 0.8165 (p)
REVERT: D  357 ILE cc_start: 0.8023 (pt) cc_final: 0.7805 (pt)
REVERT: D  360 CYS cc_start: 0.7866 (m) cc_final: 0.7601 (m)
REVERT: B 1572 ASN cc_start: 0.8278 (p0) cc_final: 0.8032 (t0)
REVERT: B 1596 MET cc_start: 0.8219 (tmm) cc_final: 0.7927 (tpp)
REVERT: B 1761 LEU cc_start: 0.8522 (mp) cc_final: 0.8244 (tt)
REVERT: B 1854 ASN cc_start: 0.8477 (t0) cc_final: 0.8042 (m-40)
REVERT: B 2690 MET cc_start: 0.7171 (ptm) cc_final: 0.6788 (ppp)
  outliers start: 5
  outliers final: 3
  residues processed: 119
  average time/residue: 0.0724
  time to fit residues: 12.6125
Evaluate side-chains
  100 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain B residue 3036 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0370
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.4858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 328 ASN
B3067 ASN
B3150 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.138133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.095620 restraints weight = 14236.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.99
r_work: 0.3289 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.0868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8439  Z= 0.130
  Angle     :  0.549   7.740  11428  Z= 0.278
  Chirality :  0.043   0.162   1322
  Planarity :  0.004   0.042   1407
  Dihedral  :  4.797  50.595   1102
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.22 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.28), residues: 1002
  helix:  2.30 (0.26), residues: 371
  sheet: -0.66 (0.31), residues: 300
  loop : -1.09 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 215 
 TYR   0.032   0.001   TYR D 320 
 PHE   0.036   0.001   PHE D 245 
 TRP   0.007   0.001   TRP D 214 
 HIS   0.005   0.001   HIS D 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 8439)
  covalent geometry    : angle       0.54872 /  0.28 (11428)
  hydrogen bonds       : bond        0.03651 /  2.39 (  368)
  hydrogen bonds       : angle       4.48532 /  3.14 ( 1053)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: D   17 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7172 (tm-30)
REVERT: D  120 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8000 (mmtt)
REVERT: D  199 TYR cc_start: 0.8154 (m-80) cc_final: 0.7796 (m-80)
REVERT: D  357 ILE cc_start: 0.7932 (pt) cc_final: 0.7674 (pt)
REVERT: D  360 CYS cc_start: 0.7742 (m) cc_final: 0.7479 (m)
REVERT: B 1572 ASN cc_start: 0.8311 (p0) cc_final: 0.8095 (t0)
REVERT: B 1596 MET cc_start: 0.8153 (tmm) cc_final: 0.7856 (tpp)
REVERT: B 1854 ASN cc_start: 0.8453 (t0) cc_final: 0.8048 (m-40)
REVERT: B 2690 MET cc_start: 0.7164 (ptm) cc_final: 0.6803 (ppp)
REVERT: B 3127 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.7872 (mtp85)
REVERT: B 3162 THR cc_start: 0.9259 (p) cc_final: 0.8907 (t)
  outliers start: 21
  outliers final: 10
  residues processed: 123
  average time/residue: 0.0846
  time to fit residues: 14.9512
Evaluate side-chains
  107 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  354 GLN
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain B residue 1611 LEU
Chi-restraints excluded: chain B residue 1791 ILE
Chi-restraints excluded: chain B residue 2676 MET
Chi-restraints excluded: chain B residue 3036 LEU
Chi-restraints excluded: chain B residue 3077 THR
Chi-restraints excluded: chain B residue 3087 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 72 optimal weight:   20.0000
   chunk 66 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0970
   chunk 52 optimal weight:    0.4980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B2625 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.139611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.093731 restraints weight = 13812.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.82
r_work: 0.3313 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8439  Z= 0.131
  Angle     :  0.566  12.084  11428  Z= 0.280
  Chirality :  0.043   0.142   1322
  Planarity :  0.004   0.040   1407
  Dihedral  :  4.463  39.674   1100
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 23.43 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.28), residues: 1002
  helix:  2.40 (0.26), residues: 371
  sheet: -0.66 (0.31), residues: 299
  loop : -1.05 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B2623 
 TYR   0.033   0.001   TYR D 320 
 PHE   0.040   0.001   PHE D 245 
 TRP   0.007   0.001   TRP D 214 
 HIS   0.004   0.001   HIS D 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 8439)
  covalent geometry    : angle       0.56577 /  0.28 (11428)
  hydrogen bonds       : bond        0.03414 /  2.24 (  368)
  hydrogen bonds       : angle       4.28173 /  3.00 ( 1053)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: D   17 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7182 (tm-30)
REVERT: D  120 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8072 (mmtt)
REVERT: D  199 TYR cc_start: 0.8135 (m-80) cc_final: 0.7775 (m-80)
REVERT: D  324 ARG cc_start: 0.5402 (OUTLIER) cc_final: 0.5187 (ttm170)
REVERT: D  344 MET cc_start: 0.6812 (ppp) cc_final: 0.6405 (ppp)
REVERT: B 1596 MET cc_start: 0.8138 (tmm) cc_final: 0.7859 (tpp)
REVERT: B 1854 ASN cc_start: 0.8416 (t0) cc_final: 0.7993 (m-40)
REVERT: B 2623 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7715 (ptt-90)
REVERT: B 2690 MET cc_start: 0.7134 (ptm) cc_final: 0.6813 (ppp)
REVERT: B 3127 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7763 (mtp85)
  outliers start: 28
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0862
  time to fit residues: 13.9944
Evaluate side-chains
  104 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  324 ARG
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain B residue 1611 LEU
Chi-restraints excluded: chain B residue 1645 SER
Chi-restraints excluded: chain B residue 1791 ILE
Chi-restraints excluded: chain B residue 2623 ARG
Chi-restraints excluded: chain B residue 2676 MET
Chi-restraints excluded: chain B residue 2684 THR
Chi-restraints excluded: chain B residue 3036 LEU
Chi-restraints excluded: chain B residue 3077 THR
Chi-restraints excluded: chain B residue 3087 LEU
Chi-restraints excluded: chain B residue 3101 THR
Chi-restraints excluded: chain B residue 3145 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 98 optimal weight:    0.0470
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0070
   chunk 15 optimal weight:    0.6980
   chunk 1 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.4333 > 50:)
   chunk 60 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   overall best weight:    0.4296

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 328 ASN
** B3067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.138185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.094894 restraints weight = 14227.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.91
r_work: 0.3305 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8439  Z= 0.120
  Angle     :  0.562  12.047  11428  Z= 0.280
  Chirality :  0.043   0.150   1322
  Planarity :  0.004   0.040   1407
  Dihedral  :  4.384  40.869   1100
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 23.87 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.28), residues: 1002
  helix:  2.40 (0.26), residues: 371
  sheet: -0.65 (0.31), residues: 299
  loop : -1.04 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B2623 
 TYR   0.035   0.001   TYR D 320 
 PHE   0.032   0.001   PHE D 245 
 TRP   0.007   0.001   TRP D 214 
 HIS   0.003   0.001   HIS B2770 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 8439)
  covalent geometry    : angle       0.56217 /  0.28 (11428)
  hydrogen bonds       : bond        0.03396 /  2.20 (  368)
  hydrogen bonds       : angle       4.24121 /  2.97 ( 1053)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: D   17 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7110 (tm-30)
REVERT: D  199 TYR cc_start: 0.8156 (m-80) cc_final: 0.7785 (m-80)
REVERT: D  344 MET cc_start: 0.6822 (ppp) cc_final: 0.6428 (ppp)
REVERT: B 1854 ASN cc_start: 0.8448 (t0) cc_final: 0.8013 (m-40)
REVERT: B 2690 MET cc_start: 0.7120 (ptm) cc_final: 0.6825 (ppp)
REVERT: B 3091 ARG cc_start: 0.8516 (tpp-160) cc_final: 0.8263 (mmt180)
  outliers start: 24
  outliers final: 16
  residues processed: 114
  average time/residue: 0.0826
  time to fit residues: 13.5506
Evaluate side-chains
  102 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain B residue 1611 LEU
Chi-restraints excluded: chain B residue 1645 SER
Chi-restraints excluded: chain B residue 1791 ILE
Chi-restraints excluded: chain B residue 2676 MET
Chi-restraints excluded: chain B residue 2684 THR
Chi-restraints excluded: chain B residue 3036 LEU
Chi-restraints excluded: chain B residue 3077 THR
Chi-restraints excluded: chain B residue 3087 LEU
Chi-restraints excluded: chain B residue 3101 THR
Chi-restraints excluded: chain B residue 3145 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 90 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 87 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0470
   overall best weight:    0.4878

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B3067 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.138173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.093025 restraints weight = 14084.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.84
r_work: 0.3304 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8439  Z= 0.128
  Angle     :  0.576  12.910  11428  Z= 0.285
  Chirality :  0.045   0.349   1322
  Planarity :  0.004   0.046   1407
  Dihedral  :  4.398  42.088   1100
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 24.30 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.28), residues: 1002
  helix:  2.38 (0.26), residues: 371
  sheet: -0.67 (0.31), residues: 299
  loop : -1.04 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B3127 
 TYR   0.039   0.001   TYR D 320 
 PHE   0.043   0.001   PHE D 245 
 TRP   0.008   0.001   TRP D 214 
 HIS   0.004   0.001   HIS B2770 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 ( 8439)
  covalent geometry    : angle       0.57634 /  0.28 (11428)
  hydrogen bonds       : bond        0.03306 /  2.13 (  368)
  hydrogen bonds       : angle       4.27215 /  3.01 ( 1053)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: D   17 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7163 (tm-30)
REVERT: D  199 TYR cc_start: 0.8124 (m-80) cc_final: 0.7782 (m-80)
REVERT: D  344 MET cc_start: 0.6799 (ppp) cc_final: 0.6454 (ppp)
REVERT: B 1854 ASN cc_start: 0.8420 (t0) cc_final: 0.8000 (m-40)
REVERT: B 2623 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6989 (pmt-80)
REVERT: B 2690 MET cc_start: 0.7157 (ptm) cc_final: 0.6828 (ppp)
  outliers start: 25
  outliers final: 16
  residues processed: 104
  average time/residue: 0.0756
  time to fit residues: 11.9666
Evaluate side-chains
  102 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain B residue 1611 LEU
Chi-restraints excluded: chain B residue 1645 SER
Chi-restraints excluded: chain B residue 1791 ILE
Chi-restraints excluded: chain B residue 2623 ARG
Chi-restraints excluded: chain B residue 2676 MET
Chi-restraints excluded: chain B residue 2684 THR
Chi-restraints excluded: chain B residue 3036 LEU
Chi-restraints excluded: chain B residue 3077 THR
Chi-restraints excluded: chain B residue 3087 LEU
Chi-restraints excluded: chain B residue 3101 THR
Chi-restraints excluded: chain B residue 3130 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0770
   chunk 41 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0870
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.4916

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.138294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.093138 restraints weight = 13991.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.84
r_work: 0.3304 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8439  Z= 0.127
  Angle     :  0.574  11.808  11428  Z= 0.284
  Chirality :  0.044   0.164   1322
  Planarity :  0.004   0.039   1407
  Dihedral  :  4.369  40.927   1100
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 24.51 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.28), residues: 1002
  helix:  2.41 (0.26), residues: 371
  sheet: -0.68 (0.31), residues: 299
  loop : -0.98 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B2623 
 TYR   0.041   0.001   TYR D 320 
 PHE   0.039   0.001   PHE D 245 
 TRP   0.008   0.001   TRP D 214 
 HIS   0.004   0.001   HIS B2770 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.13 ( 8439)
  covalent geometry    : angle       0.57437 /  0.28 (11428)
  hydrogen bonds       : bond        0.03299 /  2.12 (  368)
  hydrogen bonds       : angle       4.26153 /  3.00 ( 1053)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: D   17 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7153 (tm-30)
REVERT: D  199 TYR cc_start: 0.8125 (m-80) cc_final: 0.7761 (m-80)
REVERT: D  344 MET cc_start: 0.6843 (ppp) cc_final: 0.6504 (ppp)
REVERT: B 1854 ASN cc_start: 0.8416 (t0) cc_final: 0.8013 (m-40)
REVERT: B 2623 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7009 (pmt-80)
REVERT: B 2690 MET cc_start: 0.7154 (ptm) cc_final: 0.6830 (ppp)
  outliers start: 24
  outliers final: 18
  residues processed: 103
  average time/residue: 0.0647
  time to fit residues: 10.1564
Evaluate side-chains
  101 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  281 CYS
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain B residue 1611 LEU
Chi-restraints excluded: chain B residue 1645 SER
Chi-restraints excluded: chain B residue 1791 ILE
Chi-restraints excluded: chain B residue 2623 ARG
Chi-restraints excluded: chain B residue 2676 MET
Chi-restraints excluded: chain B residue 2684 THR
Chi-restraints excluded: chain B residue 3036 LEU
Chi-restraints excluded: chain B residue 3061 MET
Chi-restraints excluded: chain B residue 3077 THR
Chi-restraints excluded: chain B residue 3087 LEU
Chi-restraints excluded: chain B residue 3101 THR
Chi-restraints excluded: chain B residue 3130 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 82 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0980
   chunk 95 optimal weight:    0.9980
   chunk 96 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0670
   overall best weight:    0.5118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.138045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.092867 restraints weight = 14279.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.86
r_work: 0.3300 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8439  Z= 0.131
  Angle     :  0.592  14.367  11428  Z= 0.288
  Chirality :  0.045   0.382   1322
  Planarity :  0.004   0.039   1407
  Dihedral  :  4.329  38.930   1100
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.51 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.28), residues: 1002
  helix:  2.40 (0.26), residues: 371
  sheet: -0.71 (0.31), residues: 298
  loop : -0.95 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B2623 
 TYR   0.042   0.001   TYR D 320 
 PHE   0.035   0.001   PHE D 245 
 TRP   0.008   0.001   TRP D 214 
 HIS   0.004   0.001   HIS B2770 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 ( 8439)
  covalent geometry    : angle       0.59238 /  0.29 (11428)
  hydrogen bonds       : bond        0.03300 /  2.12 (  368)
  hydrogen bonds       : angle       4.23095 /  2.97 ( 1053)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 86
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: D   17 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7173 (tm-30)
REVERT: D  199 TYR cc_start: 0.8134 (m-80) cc_final: 0.7797 (m-80)
REVERT: D  344 MET cc_start: 0.6799 (ppp) cc_final: 0.6482 (ppp)
REVERT: B 1854 ASN cc_start: 0.8412 (t0) cc_final: 0.8015 (m-40)
REVERT: B 2623 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7760 (ptt-90)
REVERT: B 2690 MET cc_start: 0.7162 (ptm) cc_final: 0.6836 (ppp)
  outliers start: 27
  outliers final: 19
  residues processed: 102
  average time/residue: 0.0525
  time to fit residues: 8.3880
Evaluate side-chains
  103 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  281 CYS
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain B residue 1581 THR
Chi-restraints excluded: chain B residue 1611 LEU
Chi-restraints excluded: chain B residue 1645 SER
Chi-restraints excluded: chain B residue 1791 ILE
Chi-restraints excluded: chain B residue 2623 ARG
Chi-restraints excluded: chain B residue 2676 MET
Chi-restraints excluded: chain B residue 2684 THR
Chi-restraints excluded: chain B residue 3077 THR
Chi-restraints excluded: chain B residue 3087 LEU
Chi-restraints excluded: chain B residue 3101 THR
Chi-restraints excluded: chain B residue 3130 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 98 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B3067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.136474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.094314 restraints weight = 14228.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 3.07
r_work: 0.3268 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8439  Z= 0.179
  Angle     :  0.616  13.347  11428  Z= 0.305
  Chirality :  0.045   0.177   1322
  Planarity :  0.004   0.040   1407
  Dihedral  :  4.442  41.720   1098
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 25.05 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.28), residues: 1002
  helix:  2.25 (0.26), residues: 372
  sheet: -0.81 (0.31), residues: 298
  loop : -0.96 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B2623 
 TYR   0.043   0.002   TYR D 320 
 PHE   0.020   0.001   PHE D 245 
 TRP   0.013   0.001   TRP D 214 
 HIS   0.005   0.001   HIS B2770 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.18 ( 8439)
  covalent geometry    : angle       0.61638 /  0.31 (11428)
  hydrogen bonds       : bond        0.03495 /  2.25 (  368)
  hydrogen bonds       : angle       4.36427 /  3.08 ( 1053)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 86
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   17 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7207 (tm-30)
REVERT: D  199 TYR cc_start: 0.8199 (m-80) cc_final: 0.7799 (m-80)
REVERT: D  344 MET cc_start: 0.6777 (ppp) cc_final: 0.6468 (ppp)
REVERT: B 1854 ASN cc_start: 0.8505 (t0) cc_final: 0.8231 (m-40)
REVERT: B 2690 MET cc_start: 0.7200 (ptm) cc_final: 0.6895 (ppp)
  outliers start: 25
  outliers final: 21
  residues processed: 100
  average time/residue: 0.0603
  time to fit residues: 9.3791
Evaluate side-chains
  103 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  130 ILE
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  281 CYS
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  339 LYS
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain B residue 1581 THR
Chi-restraints excluded: chain B residue 1611 LEU
Chi-restraints excluded: chain B residue 1645 SER
Chi-restraints excluded: chain B residue 1791 ILE
Chi-restraints excluded: chain B residue 2676 MET
Chi-restraints excluded: chain B residue 2684 THR
Chi-restraints excluded: chain B residue 3077 THR
Chi-restraints excluded: chain B residue 3087 LEU
Chi-restraints excluded: chain B residue 3101 THR
Chi-restraints excluded: chain B residue 3130 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0020
   chunk 4 optimal weight:    0.0980
   chunk 17 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.4988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B3067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.137690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.092593 restraints weight = 14085.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.84
r_work: 0.3293 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8439  Z= 0.133
  Angle     :  0.632  15.187  11428  Z= 0.303
  Chirality :  0.046   0.383   1322
  Planarity :  0.004   0.058   1407
  Dihedral  :  4.366  43.645   1098
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 25.59 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.28), residues: 1002
  helix:  2.20 (0.26), residues: 371
  sheet: -0.84 (0.31), residues: 297
  loop : -0.88 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B2623 
 TYR   0.044   0.001   TYR D 320 
 PHE   0.012   0.001   PHE D 212 
 TRP   0.007   0.001   TRP B2566 
 HIS   0.004   0.001   HIS B2770 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.13 ( 8439)
  covalent geometry    : angle       0.63237 /  0.30 (11428)
  hydrogen bonds       : bond        0.03439 /  2.22 (  368)
  hydrogen bonds       : angle       4.35321 /  3.08 ( 1053)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   17 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7156 (tm-30)
REVERT: D  199 TYR cc_start: 0.8150 (m-80) cc_final: 0.7763 (m-80)
REVERT: D  344 MET cc_start: 0.6535 (ppp) cc_final: 0.6255 (ppp)
REVERT: B 1854 ASN cc_start: 0.8429 (t0) cc_final: 0.8021 (m-40)
REVERT: B 2690 MET cc_start: 0.7182 (ptm) cc_final: 0.6912 (ppp)
  outliers start: 23
  outliers final: 19
  residues processed: 102
  average time/residue: 0.0556
  time to fit residues: 8.7079
Evaluate side-chains
  105 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  281 CYS
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  339 LYS
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain B residue 1581 THR
Chi-restraints excluded: chain B residue 1611 LEU
Chi-restraints excluded: chain B residue 1645 SER
Chi-restraints excluded: chain B residue 1791 ILE
Chi-restraints excluded: chain B residue 2676 MET
Chi-restraints excluded: chain B residue 2684 THR
Chi-restraints excluded: chain B residue 3077 THR
Chi-restraints excluded: chain B residue 3087 LEU
Chi-restraints excluded: chain B residue 3101 THR
Chi-restraints excluded: chain B residue 3130 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 59 optimal weight:    0.1980
   chunk 63 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 1 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.4589 > 50:)
   chunk 53 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 99 optimal weight:    2.9990
   chunk 57 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B3067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.137346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.092315 restraints weight = 14100.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.82
r_work: 0.3285 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8439  Z= 0.148
  Angle     :  0.661  14.362  11428  Z= 0.316
  Chirality :  0.046   0.217   1322
  Planarity :  0.004   0.043   1407
  Dihedral  :  4.435  45.471   1098
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 26.03 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.28), residues: 1002
  helix:  2.14 (0.26), residues: 371
  sheet: -0.83 (0.31), residues: 298
  loop : -0.91 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B2623 
 TYR   0.047   0.002   TYR D 320 
 PHE   0.013   0.001   PHE D 212 
 TRP   0.009   0.001   TRP D 214 
 HIS   0.004   0.001   HIS B2770 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 8439)
  covalent geometry    : angle       0.66127 /  0.32 (11428)
  hydrogen bonds       : bond        0.03430 /  2.21 (  368)
  hydrogen bonds       : angle       4.41939 /  3.13 ( 1053)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2004 Ramachandran restraints generated.
    1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   17 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7199 (tm-30)
REVERT: D  199 TYR cc_start: 0.8152 (m-80) cc_final: 0.7776 (m-80)
REVERT: D  344 MET cc_start: 0.6537 (ppp) cc_final: 0.6242 (ppp)
REVERT: B 1854 ASN cc_start: 0.8430 (t0) cc_final: 0.8117 (m-40)
REVERT: B 2690 MET cc_start: 0.7192 (ptm) cc_final: 0.6899 (ppp)
REVERT: B 3164 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8941 (mm)
  outliers start: 21
  outliers final: 18
  residues processed: 102
  average time/residue: 0.0651
  time to fit residues: 10.4071
Evaluate side-chains
  104 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   45 LEU
Chi-restraints excluded: chain D residue  104 THR
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  314 TRP
Chi-restraints excluded: chain D residue  339 LYS
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain B residue 1581 THR
Chi-restraints excluded: chain B residue 1611 LEU
Chi-restraints excluded: chain B residue 1645 SER
Chi-restraints excluded: chain B residue 1791 ILE
Chi-restraints excluded: chain B residue 2676 MET
Chi-restraints excluded: chain B residue 2684 THR
Chi-restraints excluded: chain B residue 3077 THR
Chi-restraints excluded: chain B residue 3087 LEU
Chi-restraints excluded: chain B residue 3101 THR
Chi-restraints excluded: chain B residue 3130 ILE
Chi-restraints excluded: chain B residue 3164 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 48 optimal weight:    0.2980
   chunk 9 optimal weight:    0.3980
   chunk 79 optimal weight:    0.0870
   chunk 26 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 83 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.4358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 328 ASN
** B3067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.137904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.092987 restraints weight = 14083.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.82
r_work: 0.3299 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8439  Z= 0.128
  Angle     :  0.650  14.811  11428  Z= 0.310
  Chirality :  0.045   0.188   1322
  Planarity :  0.004   0.039   1407
  Dihedral  :  4.367  45.966   1098
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 26.24 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.28), residues: 1002
  helix:  2.13 (0.26), residues: 371
  sheet: -0.82 (0.31), residues: 298
  loop : -0.92 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B2623 
 TYR   0.047   0.001   TYR D 320 
 PHE   0.013   0.001   PHE D 212 
 TRP   0.012   0.001   TRP B2566 
 HIS   0.004   0.001   HIS B2770 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 8439)
  covalent geometry    : angle       0.64957 /  0.31 (11428)
  hydrogen bonds       : bond        0.03351 /  2.15 (  368)
  hydrogen bonds       : angle       4.38928 /  3.09 ( 1053)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2647.01 seconds
wall clock time: 46 minutes 2.62 seconds (2762.62 seconds total)